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Evaluation of the coarse-grained OPEP force field for protein-protein docking.


ABSTRACT: BACKGROUND:Knowing the binding site of protein-protein complexes helps understand their function and shows possible regulation sites. The ultimate goal of protein-protein docking is the prediction of the three-dimensional structure of a protein-protein complex. Docking itself only produces plausible candidate structures, which must be ranked using scoring functions to identify the structures that are most likely to occur in nature. METHODS:In this work, we rescore rigid body protein-protein predictions using the optimized potential for efficient structure prediction (OPEP), which is a coarse-grained force field. Using a force field based on continuous functions rather than a grid-based scoring function allows the introduction of protein flexibility during the docking procedure. First, we produce protein-protein predictions using ZDOCK, and after energy minimization via OPEP we rank them using an OPEP-based soft rescoring function. We also train the rescoring function for different complex classes and demonstrate its improved performance for an independent dataset. RESULTS:The trained rescoring function produces a better ranking than ZDOCK for more than 50 % of targets, rising to over 70 % when considering only enzyme/inhibitor complexes. CONCLUSIONS:This study demonstrates for the first time that energy functions derived from the coarse-grained OPEP force field can be employed to rescore predictions for protein-protein complexes.

SUBMITTER: Kynast P 

PROVIDER: S-EPMC4839147 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Evaluation of the coarse-grained OPEP force field for protein-protein docking.

Kynast Philipp P   Derreumaux Philippe P   Strodel Birgit B  

BMC biophysics 20160421


<h4>Background</h4>Knowing the binding site of protein-protein complexes helps understand their function and shows possible regulation sites. The ultimate goal of protein-protein docking is the prediction of the three-dimensional structure of a protein-protein complex. Docking itself only produces plausible candidate structures, which must be ranked using scoring functions to identify the structures that are most likely to occur in nature.<h4>Methods</h4>In this work, we rescore rigid body prote  ...[more]

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